Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. III. Photoracemization of 1-cyanoethyl cobaloxime complexes

2001 ◽  
Vol 57 (4) ◽  
pp. 551-559 ◽  
Author(s):  
Takashi Ohhara ◽  
Hidehiro Uekusa ◽  
Yuji Ohashi ◽  
Ichiro Tanaka ◽  
Shintaro Kumazawa ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Bond Cleavage ◽  
Cobalt Complexes ◽  
Crystal Form ◽  
Xenon Lamp ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Stereogenic Center ◽  
Cyanoethyl Group

The H atoms bonded to the chiral C atoms (stereogenic center) of the 1-cyanoethyl groups in two cobalt complexes, [(R)-1-cyanoethyl]bis(dimethylglyoximato)(pyridine)cobalt(III) (2) and [(R,S)-1-cyanoethyl]bis(dimethylglyoximato)(piperidine)cobalt(III) (3), were replaced with D atoms, such as Co—C*D(CH3)CN. The crystals of the two cobalt complexes were irradiated with a xenon lamp for 72 h and 27 d, respectively. The unit-cell dimensions were gradually changed with retention of the single-crystal form. The crystal structures after irradiation were determined by neutron diffraction. In each crystal the chiral 1-cyanoethyl group of one of the two crystallographically independent molecules was partly inverted to the opposite configuration, whereas that of the other molecule kept the original configuration. The C*—D bond in the inverted group was completely conserved in the process of the inversion of the chiral alkyl group. This suggests that the inversion of the chiral 1-cyanoethyl group proceeds with the rotation of the cyanoethyl radical after the Co—C bond cleavage by photo-irradiation so that the opposite side of the radical faces the Co atom. This is followed by recombination of the Co—C bond to form the inverted 1-cyanoethyl group.

Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. II. 3–1 Photoisomerization of a cobaloxime complex

2000 ◽  
Vol 56 (2) ◽  
pp. 245-253 ◽  
Author(s):  
Takashi Ohhara ◽  
Jun Harada ◽  
Yuji Ohashi ◽  
Ichiro Tanaka ◽  
Shintaro Kumazawa ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Diffraction Analysis ◽  
Crystalline State ◽  
Crystal Form ◽  
The Other ◽  
Second Step ◽  
Xenon Lamp ◽  
Disordered Structure ◽  
Cell Dimensions

Single crystal neutron diffraction analysis of photo-exposed(3-cyanopropyl-d 2 α,α)-[(R)-1-phenylethylamine-d 11]bis(dimethylglyoximato-d 14)cobalt(III) was carried out in order to clarify the mechanism of the crystalline-state photoisomerization of the 3-cyanopropyl group bonded to the Co atom in some cobaloxime complexes. Before irradiation the two H atoms bonded to the C1 atom of the 3-cyanopropyl group were exchanged with the D atoms such as —CH2CH2CD2CN. On exposure to a xenon lamp, the cell dimensions of the crystal were gradually changed. After 7 d exposure the change became insignificantly small. The structure was analyzed by neutron diffraction. The 3-cyanopropyl group was transformed to the 1-cyanopropyl group such as —CD(CN)C(H1/2,D1/2)2CH3 with retention of the single-crystal form. This indicates that one of the D atoms bonded to C1 migrates to either position bonded to C2. The other atoms of the complex remained unchanged. These results indicate that photoisomerization proceeded in two steps: the 3-cyanopropyl group was isomerized to the 2-cyanopropyl group in the first place and then the 2-cyanopropyl group was transformed to the 1-cyanopropyl group. Moreover, it was made clear that the second-step isomerization was irreversible, since one of the D atoms was retained. The disordered structure at C2 is estimated to be caused by the interconversion between the 1-cyanopropyl group produced and its dehydrogenated olefin after the photoisomerization.

Water Molecule Dispositions in the Cesium Sulfate α- and β-Alums: Single-Crystal Neutron Diffraction Studies of CsM(SO4)2.12H2O (M=V, Rh)

1993 ◽  
Vol 46 (9) ◽  
pp. 1337 ◽  
Author(s):  
JK Beattie ◽  
SP Best ◽  
FH Moore ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Neutron Diffraction ◽  
Water Molecule ◽  
Single Crystal ◽  
Tilt Angle ◽  
Room Temperature ◽  
Bond Angle ◽  
Sulfate Salt ◽  
Cell Dimensions ◽  
Coordinated Water ◽  
Unit Cell Dimensions

Room-temperature single-crystal neutron diffraction studies are recorded for two alums, Cs( Rh /V)(SO4)2.12H2O [cubic, Pa3, a 12.357(5) ( Rh ), 12.434(1)Ǻ (V)], residuals 0.037 and 0.068 for 328 and 164 'observed' reflections, with the intention of defining water molecule hydrogen atom orientations. Whereas the two tervalent hexaaqua cations are similar in size [ rM -O = 2.010(6)Ǻ (M = V) and 2.006(2)Ǻ (M = Rh )] the vanadium salt adopts the β alum modification while rhodium gives an α alum. Significantly, the water coordination geometry is different in the two cases with the tilt angle between the plane of the water molecule and the M-O bond vector being 1° (M = V) and 35° (M = Rh ). The tilt angle for water coordinated to rhodium in CsRh (SeO4)2.12H2O is inferred from the unit cell dimensions to be similar to that of the corresponding sulfate salt and not that which generally pertains for caesium selenate alums. Significant differences in the H-O-H bond angle are found for trigonal planar and trigonal pyramidal water coordination, suggesting that differences in the metal(III)-water interaction are a determinant of the geometry of the coordinated water molecule in the caesium sulfate/ selenate alum lattices.

Crystallization and preliminary X-ray crystallographic analysis of the Pseudomonas aeruginosa cyclohexadienyl dehydratase

1999 ◽  
Vol 55 (2) ◽  
pp. 539-541
Author(s):  
Palangpon Kongsaeree ◽  
Jun Liang ◽  
Roy A. Jensen ◽  
Jon Clardy
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Crystal Form ◽  
High Energy ◽  
Crystallographic Analysis ◽  
Unit Cell ◽  
Space Group ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The title protein has been crystallized in a new crystal form. The crystals belong to the cubic space group P4132 (or P4332) with unit-cell dimensions a = b = c = 126.1 Å at 100 K and typically diffract beyond 1.6 Å at the Cornell High Energy Synchotron Source (CHESS) A1 beamline.

Powder X-ray diffraction data for Ba4ZnTi11O27 and Ba2ZnTi5O13

1994 ◽  
Vol 9 (1) ◽  
pp. 56-62 ◽  
Author(s):  
C. G. Lindsay ◽  
C. J. Rawn ◽  
R. S. Roth
Keyword(s):  
Single Crystal ◽  
Single Crystals ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Lattice Parameters ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Powder Samples ◽  
Unit Cell Dimensions

Single crystals and powder samples of Ba4ZnTi11O27 and Ba2ZnTi5O13 have been synthesized and studied using single-crystal X-ray precession photographs and X-ray powder diffraction. Unit cell dimensions were calculated from a least-squares refinement with a final maximum Δ2θ of 0.05°. Both phases were found to have monoclinic cells, space group C2/m. The refined lattice parameters for the Ba4ZnTi11O27 compound are a= 19.8687(8) Å, b=11.4674(5) Å, c=9.9184(4) Å, β= 109.223(4)°, and Z=4. The refined lattice parameters for the Ba2ZnTi5O13 compound are a= 15.2822(7) Å, b=3.8977(1) Å, c=9.1398(3) Å, β=98.769(4)°, and Z=2.

scholarly journals The reaction of 3,5-diphenyl-1,2-dithiolium-4-olate with aniline: the crystal structure of 1-phenylimino-2-phenylamino-3-phenylindene

1987 ◽  
Vol 65 (12) ◽  
pp. 2830-2833 ◽  
Author(s):  
David M. McKinnon ◽  
Peter D. Clark ◽  
Robert O. Martin ◽  
Louis T. J. Delbaere ◽  
J. Wilson Quail
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Single Crystal ◽  
Least Squares ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

3,5-Diphenyl-1,2-dithiolium-4-olate (1) reacts with aniline to form 1-phenylimino-2-phenylamino-3-phenylindene (3a). Under suitable conditions, 6-phenylbenzo[b]indeno[1,2-e]-1,2-thiazine is also formed. These structures are confirmed by alternative syntheses. The molecular structure of 3a has been determined by single crystal X-ray diffraction. Compound 3a crystallizes in the monoclinic space group C2/c with unit cell dimensions a = 20.777(3) Å, b = 6.130(3) Å, c = 31.327(3) Å, 3 = 99.59(1)°, and Z = 8. The structure was solved by direct methods and refined by least squares to a final R = 0.055. The molecular structure of 3a shows the three phenyl containing substituents to have the planes of their ring systems tilted between 40° and 60° from the plane of the indene system due to steric repulsions.

scholarly journals Synthesis, Crystal Structure, and DFT Calculations of 1,3-Diisobutyl Thiourea

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Ataf A. Altaf ◽  
Adnan Shahzad ◽  
Zarif Gul ◽  
Sher A. Khan ◽  
Amin Badshah ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Dft Calculations ◽  
Single Crystal ◽  
Crystal Packing ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Model Support

1,3-Diisobutyl thiourea was synthesized and characterized by single crystal X-ray diffraction. It gives a monoclinic (α=γ= 90 andβ  ≠90) structure with the space group P21/c. The unit cell dimensions area= 11.5131 (4) Å,b= 9.2355 (3) Å,c= 11.3093 (5) Å,α= 90°,β= 99.569° (2),γ= 90°,V= 1185.78 (8) Å3, andZ= 4. The crystal packing is stabilized by intermolecular (N–H⋯S) hydrogen bonding in the molecules. The optimized geometry and Mullikan's charges of the said molecule calculated with the help of DFT using B3LYP-6-311G model support the crystal structure.

Structure of an insulin dimer in an orthorhombic crystal: the structure analysis of a human insulin mutant (B9 Ser→Glu)

1999 ◽  
Vol 55 (9) ◽  
pp. 1524-1532 ◽  
Author(s):  
Zhi-Ping Yao ◽  
Zong-Hao Zeng ◽  
Hong-Min Li ◽  
Ying Zhang ◽  
You-Min Feng ◽  
...  
Keyword(s):  
Human Insulin ◽  
Solution Structure ◽  
Building Blocks ◽  
Structural Rearrangement ◽  
Crystal Form ◽  
Terminal Segment ◽  
Orthorhombic Crystal ◽  
Amino Terminal ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The structure of human insulin mutant B9 (Ser→Glu) was determined by an X-ray crystallographic method at 2.5 Å resolution with an R factor of 0.165 under non-crystallographic restraints. The crystals were grown at low pH (<3.8) and belong to the orthorhombic P212121 space group with unit-cell dimensions a = 44.54, b = 46.40, c = 51.85 Å and one dimer per asymmetric unit without further aggregation. The structure in this crystal form can be regarded as a model for a discrete insulin dimer and displays the following features compared with the structure of 2Zn insulin. (i) The overall dimer is expanded and more symmetric. The two A chains are about 2 Å more distant from each other, while the two B chains are about 0.8 Å further apart. Both monomers are more similar to molecule 1 than molecule 2 of the 2Zn insulin dimer. (ii) The dimer structure is stabilized by protonation and neutralization of the carboxyl groups at lower pH and, in addition, by formation of a hydrogen-bond network among the side chains of residues GluB9, HisB13 and HisB10 on the dimer-forming surface of both monomers, resulting from a structural rearrangement. (iii) The B-chain amino-terminal segment is in an open state (O state), i.e. a state different from the well known R and T states found in the insulin hexamer. In the O state, the B-chain N-terminal segment is in an extended conformation and is detached from the rest of the molecule. This conformational state has also been observed in the monomeric crystal structure of despentapeptide (B26–B30) and desheptapeptide (B24–B30) insulin, as well as in the solution structure of an engineered insulin monomer. It suggests that the O state may be the characteristic conformation of insulin in lower aggregation forms and may be relevant to the formation of insulin fibrils. In addition, based on the crystallization process, the smallest possible building blocks of insulin crystal are also discussed.

Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27

2019 ◽  
Vol 52 (5) ◽  
pp. 972-983 ◽  
Author(s):  
Taro Yamada ◽  
Naomine Yano ◽  
Takaaki Hosoya ◽  
Katsuhiro Kusaka
Keyword(s):  
Oxygen Atom ◽  
Single Crystal ◽  
Thermus Thermophilus ◽  
Time Of Flight ◽  
Unit Cell ◽  
Intensity Data ◽  
Diffraction Intensity ◽  
Manganese Catalase ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The IBARAKI biological crystal diffractometer (iBIX) was used in single-crystal time-of-flight neutron diffraction experiments on manganese catalase from Thermus thermophilus. The unit-cell dimensions were 133 × 133 × 133 Å, which is close to the designed maximum limitation of iBIX (135 × 135 × 135 Å). The optimum integration box sizes were set and the degree of integration box overlap was calculated for each Laue spot. Using the overlap ratio as the criterion, the selection of the diffraction intensity data was performed to give a minimum R p.i.m.. Subsequently, diffraction intensity data from Laue spots with overlap ratios ≤0.1 were selected and a complete reflection data set with d min = 2.35 Å was obtained. Joint X-ray and neutron structure refinements were also successfully performed. It was difficult to determine the structures and protonation states of all the oxygen atoms in the manganese cluster owing to the disordered structure. No hydrogen atom was observed on the ordered μ-bridging oxygen atom O1003. Instead, this oxygen atom probably forms a hydrogen bond with Thr39. In addition, the refinements clearly showed the protonation states of the amino acid residues and hydrogen bonds, as observed in Tyr192, Glu167 and Glu280. This first neutron crystal structure of manganese catalase shows that iBIX can provide acceptable diffraction data for neutron single-crystal analyses of at least 2.4 Å resolution within the original targeted unit-cell dimensions of 135 × 135 × 135 Å.

The högbomite polytypes

1963 ◽  
Vol 33 (262) ◽  
pp. 563-580 ◽  
Author(s):  
Duncan McKie
Keyword(s):  
Single Crystal ◽  
Unit Cell ◽  
Stacking Sequence ◽  
X Ray ◽  
Hexagonal Unit Cell ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

SummarySingle crystal X-ray examination has shown that högbomite forms a series of polytypes, designated nH or nR, with hexagonal or rhombohedral lattices and hexagonal unit-cell dimensions a 5·72 Å, c 4·6 × n Å. The polytypes arise by variation, in a manner as yet undetermined, of the stacking sequence of approximately close-packed oxygen layers with interstitial cations on fourfold and on sixfold sites; the composition of 1/nth of a unit-cell may be represented as R2+1.0_1.6T4+0.2-0.4R3+3.7-4.3O2-7.6-8.0(OH)-0-0.4,, where R2+ = Zn, Fe, Mg, and R2+ = Fe, Al. The polytypes so far observed are 4H, 5H, 6H, 15H, 15R, and 18R. Minerals structurally related to högbomite are nigerite (3H) and taaffeite (4H). A new occurrence of högbomite, polytype 5H, with composition Ti1·7Fe1·6Mg6·3Al18·8Si0·2O40, is described from a spinel-free paragenesis in a magnesian skarn at Mautia Hill, Tanganyika. Another new occurrence in an aluminous xenolith in the Cashel gabbro in Co. Galway, Ireland, is recorded. X-ray powder data are given for two of the polytypes.

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